[gmx-users] About Physical parameters

[Justin Lemkul]

On 6/4/13 8:22 AM, vidhya sankar wrote:
>
>
> Dear Justin Thank you for your Previuos reply
>
>                                                                                  I am using gromos53a6 ff When i changed the parameters for cut-off  (r list ) value to 1.2
>
> I have got Error as follows  What is the Meaning of Note 2 & 3
>
>
> NOTE 2 [file cntcycpepfull2.mdp]:
>    The switch/shift interaction settings are just for compatibility; you
>    will get betterperformance from applying potential modifiers to your
>    interactions!
>
> NOTE 3 [file cntcycpepfull2.mdp]:
>    For energy conservation with switch/shift potentials, rlist should be 0.1
>    to 0.3 nm larger than rcoulomb.
> NOTE 4 [file cntcycpepfull2.mdp]:
>    For energy conservation with switch/shift potentials, rlist should be 0.1
>    to 0.3 nm larger than rvdw.
>
> WARNING 1 [file cntcycpepfull2.mdp]:
>    The sum of the two largest charge group radii (0.518710) is larger than
>    rlist (1.200000) - rvdw (1.200000)
>
> WARNING 2 [file cntcycpepfull2.mdp]:
>    The sum of the two largest charge group radii (0.518710) is larger than
>    rlist (1.200000) - rcoulomb (1.200000)
>
> nstlist        = 5
>
> rlist        = 1.2
> rcoulomb    = 1.2
>
> vdwtype         = Shift
> rvdw        = 1.2
> coulombtype    =  Reaction-Field-zero
>
> pme_order    = 4
> fourierspacing    = 0.16
> pcoupl        = Parrinello-Rahman
>
> pcoupltype    = isotropic
>
> thus .grompp terminated due to warnings
>
> To Avoid his I have used the rlist=1.8 (in Above valuue) Because the difference betwen rlist-rcoloum should Be greater than 0.518710
>
> But you maild me the cut-off looks Bizarre .it should be based on parent force field(mine is gromos53a6)
>

If you're using Gromos96 53A6, nearly all of your settings are wrong.  Please 
refer to the primary literature for the force field and the many posts in the 
list archive regarding proper use of that force field.  Making ad hoc changes 
just to get grompp to stop complaining is a very error-prone way to do 
simulations (which end up being unstable or invalid by doing so).

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================